Refactoring earnaud#6

NAMESPACE

@@ -3,6 +3,8 @@
 export(runMetashark)
 export(write.text)
 import(shiny)
+import(shinydashboard)
+import(shinydashboardPlus)
 importFrom(EML,eml_validate)
 importFrom(EML,get_unitList)
 importFrom(EML,read_eml)
@@ -66,8 +68,6 @@ importFrom(shinyFiles,shinyFilesButton)
 importFrom(shinyTree,get_selected)
 importFrom(shinyTree,renderTree)
 importFrom(shinyTree,shinyTree)
-importFrom(shinycssloaders,withSpinner)
-importFrom(shinydashboard,box)
 importFrom(shinydashboard,dashboardBody)
 importFrom(shinydashboard,dashboardHeader)
 importFrom(shinydashboard,dashboardPage)

R/about-module.R

@@ -1,22 +1,73 @@
+#' @import shiny
+#'
+#' @noRd
+aboutUI <- function(id) {
+  ns <- NS(id)
+
+  fluidPage(
+    tags$h1("About MetaShARK dev team"),
+    HTML("MetaShARK is developped within the french Museum National 
+          d'Histoire Naturelle / UMS Patrimoine Naturel / Pole 
+          National de Biodiversite. Its development team is currently
+          composed of <a href='https://fr.linkedin.com/in/elie-arnaud-440132151?trk=people-guest_profile-result-card_result-card_full-click'>Elie Arnaud</a>
+          (lead developer) and <a href ='https://fr.linkedin.com/in/yvan-le-bras-aa2b3738?trk=people-guest_profile-result-card_result-card_full-click'>Yvan Le Bras</a> (team director)."),
+
+    tags$h1("Thanks"),
+    HTML("MetaShARK could not be built without the help of those people: </br>
+        <ul>
+          <li>Colin Smith (EDI, US)</li> who collaborates with us since March 
+          2019, and currently provides us the <a href='https://github.com/EDIorg/EMLassemblyline'>EML Assembly Line</a> tool.
+        </ul>"),
+
+    tags$h1("References"),
+    # Parties
+    tags$h2("LTER and EML Actors"),
+    tags$p("The following people and parties have worked upstream of
+      MetaShARK dev team to provide the fundamentals united in
+      the present tool."),
+    uiOutput(NS(id, "actors")),
+    # Informatics
+    tags$h2("Computer material"),
+    tags$p("The following references will lead the user to the source
+      of tools and methods reused in MetaShARK."),
+    uiOutput(NS(id, "informatics")),
+    # Sci litt
+    tags$h2("Literature"),
+    tags$p("MetaShARK is based on the following papers and articles
+      concerning mainly ecological metadata."),
+    uiOutput(NS(id, "ecology"))
+  )
+}
+
 #' @title about
 #'
 #' @description server part of the about module.
-#' 
+#'
 #' @import shiny
-#' 
+#'
 #' @noRd
-about <- function(input, output, session) {
-  ns <- session$ns
+about <- function(id) {
+  moduleServer(id, function(input, output, session) {
 
-  .bibliography <- reactiveValues(
-    actors = system.file("resources/bibliography-actors.bib", package = "MetaShARK"),
-    informatics = system.file("resources/bibliography-informatics.bib", package = "MetaShARK"),
-    ecology = system.file("resources/bibliography-ecology.bib", package = "MetaShARK"),
-    misc = system.file("resources/bibliography-misc.bib", package = "MetaShARK")
-  )
+    # misc = system.file("resources/bibliography-misc.bib", package = "MetaShARK")
 
-  # use function
-  output$actors <- renderBibliography(.bibliography$actors)
-  output$informatics <- renderBibliography(.bibliography$informatics)
-  output$ecology <- renderBibliography(.bibliography$ecology)
+    output$actors <- renderBibliography(
+      system.file(
+        "resources/bibliography-actors.bib",
+        package = "MetaShARK"
+      )
+    )
+    output$informatics <- renderBibliography(
+      system.file(
+        "resources/bibliography-informatics.bib",
+        package = "MetaShARK"
+      )
+    )
+    output$ecology <- renderBibliography(
+      system.file(
+        "resources/bibliography-ecology.bib",
+        package = "MetaShARK"
+      )
+    )
+  })
 }

R/about-module_functions.R

@@ -10,7 +10,7 @@
 #' @importFrom utils capture.output
 renderBibliography <- function(bib) {
   .bib <- RefManageR::ReadBib(bib)
-  RefManageR::NoCite(bib, "*")
+  RefManageR::NoCite(.bib, "*")
 
   renderUI(
     withProgress(message = "Loading bibtex ...", value = 0, {

R/documentation-module.R

@@ -1,7 +1,6 @@
 #' @import shiny
-#' @importFrom shinydashboard box
 #' @importFrom shinyTree shinyTree
-#' 
+#'
 #' @noRd
 docUI <- function(id) {
   ns <- NS(id)
@@ -23,17 +22,16 @@ docUI <- function(id) {
           shinyTree::shinyTree(
             outputId = NS(id, "tree"),
             search = TRUE,
-            theme = "proton"
+            theme = "proton",
+            wholerow = TRUE,
+            multiple = FALSE
           )
         )
       ),
       # display main panel
       column(
         7,
-        div(
-          id = "docPanel",
-          uiOutput(NS(id, "doc"))
-        )
+        uiOutput(NS(id, "doc"))
       )
     )
   )
@@ -42,40 +40,45 @@ docUI <- function(id) {
 #' @import shiny
 #' @importFrom shinyTree renderTree get_selected
 #' @importFrom jsonlite read_json unserializeJSON
-#' 
+#'
 #' @noRd
-documentation <- function(input, output, session) {
-  ns <- session$ns
+documentation <- function(id) {
+  moduleServer(id, function(input, output, session) {
 
-  # Load data ====
-  withProgress(message = "Loading documentation.", {
-    doc <- system.file("resources/doc_guideline.json", package = "MetaShARK") %>%
-      jsonlite::read_json(simplifyVector = TRUE) %>%
-      jsonlite::unserializeJSON()
-    incProgress(0.5)
-    tree <- system.file("resources/tree_guideline.json", package = "MetaShARK") %>%
-      jsonlite::read_json(simplifyVector = TRUE) %>%
-      jsonlite::unserializeJSON()
-    incProgress(0.5)
-  })
+    # Load data ====
+    doc <- system.file("resources/doc_guideline.json", package = "MetaShARK")
+    doc <- jsonlite::unserializeJSON(jsonlite::read_json(doc)[[1]])
 
-  # UI render ====
+    tree <- system.file("resources/tree_guideline.json", package = "MetaShARK")
+    tree <- jsonlite::unserializeJSON(jsonlite::read_json(tree)[[1]])
 
-  # render tree
-  output$tree <- shinyTree::renderTree(tree)
+    # UI render ====
 
-  # output selected node
-  output$doc <- renderUI({
-    tree.node <- shinyTree::get_selected(input$tree)
-    validate(
-      need(unlist(tree.node), "(Select an item first)")
-    )
-    path <- paste(c(attr(tree.node[[1]], "ancestry"), unlist(tree.node)), collapse = "/")
-    doc.node <- followPath(doc, path)
-    if ("annotation" %in% names(doc.node)) {
-      doc.node$annotation
-    } else {
-      helpText("No content found at:", path)
-    }
+    # render tree
+    output$tree <- shinyTree::renderTree({
+      tree
+    })
+
+    # output selected node
+    output$doc <- renderUI({
+      req("tree" %in% names(input))
+      tree.node <- get_selected(input$tree)
+      validate(
+        need(unlist(tree.node), "(Select an item first)")
+      )
+      path <- paste(
+        c(
+          attr(tree.node[[1]], "ancestry"),
+          unlist(tree.node)
+        ),
+        collapse = "/"
+      )
+      doc.node <- followPath(doc, path)
+      if ("annotation" %in% names(doc.node)) {
+        doc.node$annotation
+      } else {
+        helpText("No content found at:", path)
+      }
+    })
   })
 }